Some parts of Japanese mega cities such as Tokyo, Nagoya and Osaka are below sea level and these areas are prone to floods. These three areas are in coastal zone and over 1000 people were sacrificed by storm surge in the past time. Inundation of underground spaces by pluvial and tsunami flood in the center of Osaka have been investigated in our previous works. Underground inundation by storm surge caused by super typhoon is discussed in this paper. The results show that 50 percent of total overflow discharge intrudes into underground spaces. Almost all amount of intruding discharge into underground mall fall down to the subway stations connected to the mall. The damage is different from the results caused by pluvial and tsunami floods. This means that administrators of underground space have to make different countermeasures for each disaster.